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- PDB-1b0o: BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH PALMITATE, LATTICE Z -

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Basic information

Entry
Database: PDB / ID: 1b0o
TitleBOVINE BETA-LACTOGLOBULIN COMPLEXED WITH PALMITATE, LATTICE Z
ComponentsBETA-LACTOGLOBULIN
KeywordsLIPOCALIN / MILK WHEY PROTEIN / BOVINE / PALMITATE-BINDING
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, S.-Y. / Sawyer, L.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: beta-lactoglobulin binds palmitate within its central cavity.
Authors: Wu, S.Y. / Perez, M.D. / Puyol, P. / Sawyer, L.
#1: Journal: Biochemistry / Year: 1998
Title: Structural Basis of the Tanford Transition of Bovine Beta-Lactoglobulin
Authors: Qin, B.Y. / Bewley, M.C. / Creamer, L.K. / Baker, H.M. / Baker, E.N. / Jameson, G.B.
#2: Journal: Structure / Year: 1997
Title: Bovine Beta-Lactoglobulin at 1.8 A Resolution--Still an Enigmatic Lipocalin
Authors: Brownlow, S. / Morais Cabral, J.H. / Cooper, R. / Flower, D.R. / Yewdall, S.J. / Polikarpov, I. / North, A.C. / Sawyer, L.
#3: Journal: FEBS Lett. / Year: 1998
Title: 12-Bromododecanoic Acid Binds Inside the Calyx of Bovine Beta-Lactoglobulin
Authors: Qin, B.Y. / Creamer, L.K. / Baker, E.N. / Jameson, G.B.
History
DepositionNov 11, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5582
Polymers18,3011
Non-polymers2561
Water1,892105
1
A: BETA-LACTOGLOBULIN
hetero molecules

A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1154
Polymers36,6022
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)53.480, 53.480, 111.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-LACTOGLOBULIN


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PROTEIN PURCHASED FROM SIGMA CHEMICALS, LOT 13H7150
Source: (natural) Bos taurus (domestic cattle) / Cellular location: EXTRACELLULAR / Organ: MAMMARY GLAND / Secretion: MILK / Variant: GENETIC VARIANT B / References: UniProt: P02754
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 50.78 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
2100 mMpalmitic acid1drop
41.34 Msodium citrate1reservoir
50.1 MHEPES1reservoir
1protein1dropa molar ratio of 10/protein dimer
3ethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 6888 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.16 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.95 / % possible all: 100
Reflection
*PLUS
Num. measured all: 97142
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEB

1beb


Resolution: 2.5→10 Å / Num. parameters: 5583 / Num. restraintsaints: 5396 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 336 5 %RANDOM
obs0.2049 -99.9 %-
all-6685 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1395
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 18 105 1395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0.007
X-RAY DIFFRACTIONs_from_restr_planes0.28
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.17 Å2

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